#ifndef __itkMultiResolutionLogDomainDeformableRegistration_h
#define __itkMultiResolutionLogDomainDeformableRegistration_h

#include "itkExponentialDisplacementFieldImageFilter.h"
#include "itkImage.h"
#include "itkImageToImageFilter.h"
#include "itkLogDomainDeformableRegistrationFilter.h"
#include "itkLogDomainDemonsRegistrationFilter.h"
#include "itkMultiResolutionPyramidImageFilter.h"
#include "itkResampleImageFilter.h"

#include <vector>

namespace itk
{
/**
 * \class MultiResolutionLogDomainDeformableRegistration
 * \brief Framework for performing multi-resolution log-domain
 * deformable registration.
 *
 * MultiResolutionLogDomainDeformableRegistration provides a generic framework
 * to peform multi-resolution deformable registration.
 *
 * At each resolution level a LogDomainDeformableRegistrationFilter is used
 * to register two images by computing the velocity field whose exponential will
 * map a moving image onto a fixed image.
 *
 * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
 * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
 * Proc. of MICCAI 2008.
 *
 * Velocity and deformation fields are represented as images whose pixel type is some
 * vector type with at least N elements, where N is the dimension of
 * the fixed image. The vector type must support element access via operator
 * []. It is assumed that the vector elements behave like floating point
 * scalars.
 *
 * The internal LogDomainDeformableRegistrationFilter can be set using
 * SetRegistrationFilter. By default a LogDomainDemonsRegistrationFilter is used.
 *
 * The input fixed and moving images are set via methods SetFixedImage
 * and SetMovingImage respectively. An initial velocity field maybe set via
 * SetInitialVelocityField if is matches the characteristics of the coarsest
 * pyramid level. If no such assumption can be made (e.g. the velocity field
 * has the same characteristics as the input images), an initial velocity
 * field can still be set via SetArbitraryInitialVelocityField or
 * SetInput. The filter will then take care of mathching the coarsest level
 * characteristics. If no initial field is set a zero field is used as the
 * initial condition.
 *
 * MultiResolutionPyramidImageFilters are used to downsample the fixed
 * and moving images. A VectorExpandImageFilter is used to upsample
 * the velocity field as we move from a coarse to fine solution.
 *
 * This class is templated over the fixed image type, the moving image type,
 * and the velocity/deformation Field type.
 *
 * \warning This class assumes that the fixed, moving and
 * field image types all have the same number of dimensions.
 *
 * \author Florence Dru, INRIA and Tom Vercauteren, MKT
 *
 * \sa LogDomainDeformableRegistrationFilter
 * \sa LogDomainDemonsRegistrationFilter
 * \sa MultiResolutionPyramidImageFilter
 * \sa VectorExpandImageFilter
 *
 * The current implementation of this class does not support streaming.
 *
 * \ingroup DeformableImageRegistration
 */
template <class TFixedImage, class TMovingImage, class TField, class  TRealType = float>
class ITK_EXPORT MultiResolutionLogDomainDeformableRegistration :
  public ImageToImageFilter<TField, TField>
{
public:
  /** Standard class typedefs */
  typedef MultiResolutionLogDomainDeformableRegistration Self;
  typedef ImageToImageFilter<TField, TField>
  Superclass;
  typedef SmartPointer<Self>       Pointer;
  typedef SmartPointer<const Self> ConstPointer;

  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** Run-time type information (and related methods). */
  itkTypeMacro( MultiResolutionLogDomainDeformableRegistration,
                ImageToImageFilter );

  /** Fixed image type. */
  typedef TFixedImage                           FixedImageType;
  typedef typename FixedImageType::Pointer      FixedImagePointer;
  typedef typename FixedImageType::ConstPointer FixedImageConstPointer;

  /** Moving image type. */
  typedef TMovingImage                           MovingImageType;
  typedef typename MovingImageType::Pointer      MovingImagePointer;
  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;

  /** Velocity field type. */
  typedef TField                              VelocityFieldType;
  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;

  /** Deformation field image type. */
  typedef TField                                 DeformationFieldType;
  typedef typename DeformationFieldType::Pointer DeformationFieldPointer;

  /** ImageDimension. */
  itkStaticConstMacro(ImageDimension, unsigned int,
                      FixedImageType::ImageDimension);

  /** Internal float image type. */
  typedef Image<TRealType, itkGetStaticConstMacro(ImageDimension)> FloatImageType;

  /** The internal registration type. */
  typedef LogDomainDeformableRegistrationFilter<FloatImageType, FloatImageType, VelocityFieldType>
  RegistrationType;
  typedef typename RegistrationType::Pointer RegistrationPointer;

  /** The default registration type. */
  typedef LogDomainDemonsRegistrationFilter<
    FloatImageType, FloatImageType, VelocityFieldType> DefaultRegistrationType;

  /** The fixed multi-resolution image pyramid type. */
  typedef MultiResolutionPyramidImageFilter<FixedImageType, FloatImageType>
  FixedImagePyramidType;
  typedef typename FixedImagePyramidType::Pointer FixedImagePyramidPointer;

  /** The moving multi-resolution image pyramid type. */
  typedef MultiResolutionPyramidImageFilter<MovingImageType, FloatImageType>
  MovingImagePyramidType;
  typedef typename MovingImagePyramidType::Pointer MovingImagePyramidPointer;

  /** The velocity field expander type. */
  typedef ResampleImageFilter<VelocityFieldType, VelocityFieldType>
  FieldExpanderType;
  typedef typename FieldExpanderType::Pointer FieldExpanderPointer;

  /** Set the fixed image. */
  virtual void SetFixedImage( const FixedImageType * ptr );

  /** Get the fixed image. */
  const FixedImageType * GetFixedImage(void) const;

  /** Set the moving image. */
  virtual void SetMovingImage( const MovingImageType * ptr );

  /** Get the moving image. */
  const MovingImageType * GetMovingImage(void) const;

  /** Set initial velocity field to be used as is (no smoothing, no
   *  subsampling at the coarsest level of the pyramid. */
  virtual void SetInitialVelocityField( VelocityFieldType * ptr )
  {
    this->m_InitialVelocityField = ptr;
  }

  /** Set initial velocity field. No assumption is made on the
   *  input. It will therefore be smoothed and resampled to match the
   *  images characteristics at the coarsest level of the pyramid. */
  virtual void SetArbitraryInitialVelocityField( VelocityFieldType * ptr )
  {
#if (ITK_VERSION_MAJOR < 4)
    this->SetNthInput(VELOCITYFIELD_IMAGE_CODE, ptr );
#else
    this->SetNthInput(VELOCITYFIELD_IMAGE_CODE, ptr);
#endif
  }

  /**
   * Sets the regularization type.
   * @param  value  maximum length
   */
  void                                   SetRegularizationType(unsigned int regularizationType) ;


  /**
   * Gets the regularization type.
   * @return  regularization type
   */
  unsigned int                           GetRegularizationType(void);

  /**
   * Sets the weight for the penalization of the harmonic energy.
   * @param  harmonic weight
   */
  void                                   SetHarmonicWeight(float harmonicWeight) ;

  /**
   * Gets the weight for the penalization of the harmonic energy.
   * @return  harmonic weight
   */
  float                                  GetHarmonicWeight(void);

  /**
   * Sets the weight for the penalization of the bending energy.
   * @param  harmonic weight
   */
  void                                   SetBendingWeight(float bendingWeight) ;

  /**
   * Gets the weight for the penalization of the bending energy.
   * @return  bending weight
   */
  float                                  GetBendingWeight(void);


  /** Get output velocity field. */
  VelocityFieldType * GetVelocityField()
  {
    return this->GetOutput();
  }

  /** Get output deformation field. */
  DeformationFieldPointer GetDeformationField();

  /** Get output inverse deformation field. */
  DeformationFieldPointer GetInverseDisplacementField();

  /** Get the number of valid inputs.  For
   * MultiResolutionLogDomainDeformableRegistration, this checks whether the
   * fixed and moving images have been set. While
   * MultiResolutionLogDomainDeformableRegistration can take a third input
   * as an initial velocity field, this input is not a required input. */
  virtual std::vector<SmartPointer<DataObject> >::size_type GetNumberOfValidRequiredInputs() const;

  /** Set the internal registrator. */
  itkSetObjectMacro( RegistrationFilter, RegistrationType );

  /** Get the internal registrator. */
  itkGetObjectMacro( RegistrationFilter, RegistrationType );

  /** Set the fixed image pyramid. */
  itkSetObjectMacro( FixedImagePyramid, FixedImagePyramidType );

  /** Get the fixed image pyramid. */
  itkGetObjectMacro( FixedImagePyramid, FixedImagePyramidType );

  /** Set the moving image pyramid. */
  itkSetObjectMacro( MovingImagePyramid, MovingImagePyramidType );

  /** Get the moving image pyramid. */
  itkGetObjectMacro( MovingImagePyramid, MovingImagePyramidType );

  /** Set number of multi-resolution levels. */
  virtual void SetNumberOfLevels( unsigned int num );

  /** Get number of multi-resolution levels. */
  itkGetConstReferenceMacro( NumberOfLevels, unsigned int );

  /** Get the current resolution level being processed. */
  itkGetConstReferenceMacro( CurrentLevel, unsigned int );

  /** Set number of iterations per multi-resolution levels. */
  itkSetVectorMacro( NumberOfIterations, unsigned int, m_NumberOfLevels );

  /** Set the moving image pyramid. */
  itkSetObjectMacro( FieldExpander, FieldExpanderType );

  /** Get the moving image pyramid. */
  itkGetObjectMacro( FieldExpander, FieldExpanderType );

  /** Get number of iterations per multi-resolution levels. */
  virtual const unsigned int * GetNumberOfIterations() const
  {
    return &(m_NumberOfIterations[0]);
  }

  /** Stop the registration after the current iteration. */
  virtual void StopRegistration();
  
  
  /**
   * Sets the standard deviation (world unit) used for the global field regularization.
   * @param  value  standard deviation
   */
  virtual void SetStandardDeviationsWorldUnit( double value );


  /**
   * Sets the standard deviation (world unit) used for the global field regularization.
   * @param  value  standard deviation
   */
  virtual void SetStandardDeviationsWorldUnit( double value[] );


  /**
   * Sets the standard deviation (voxel unit) used for the global field regularization.
   * @param  value  standard deviation
   */
  virtual void SetStandardDeviationsVoxelUnit( double value );


  /**
   * Sets the standard deviation (voxel unit) used for the global field regularization.
   * @param  value  standard deviation
   */
  virtual void SetStandardDeviationsVoxelUnit( double value[] );


  /**
   * Gets the standard deviation used for the global field regularization.
   */
  const double * GetStandardDeviations(void) const
  {
      return static_cast<const double*>( this->m_StandardDeviations );
  }


  /**
   * Sets if the velocity field is smoothed or not
   */
  itkSetMacro( SmoothVelocityField, bool );
  itkGetConstMacro( SmoothVelocityField, bool );
  itkBooleanMacro( SmoothVelocityField );


  /**
   * Sets the standard deviation (world unit) used for the update field regularization.
   * @param  value  standard deviation
   */
  virtual void SetUpdateFieldStandardDeviationsWorldUnit( double value );


  /**
   * Sets the standard deviation (world unit) used for the update field regularization.
   * @param  value  standard deviation
   */
  virtual void SetUpdateFieldStandardDeviationsWorldUnit( double value[] );


  /**
   * Sets the standard deviation (voxel unit) used for the update field regularization.
   * @param  value  standard deviation
   */
  virtual void SetUpdateFieldStandardDeviationsVoxelUnit( double value );


  /**
   * Sets the standard deviation (voxel unit) used for the update field regularization.
   * @param  value  standard deviation
   */
  virtual void SetUpdateFieldStandardDeviationsVoxelUnit( double value[] );


  /**
   * Gets the standard deviation used for the update field regularization.
   */
  const double * GetUpdateFieldStandardDeviations(void) const
  {
      return static_cast<const double*>( this->m_UpdateFieldStandardDeviations );
  }



  /**
   * Sets if the velocity field is smoothed or not
   */
  itkSetMacro( SmoothUpdateField, bool );
  itkGetConstMacro( SmoothUpdateField, bool );
  itkBooleanMacro( SmoothUpdateField );


  

protected:
  MultiResolutionLogDomainDeformableRegistration();
  ~MultiResolutionLogDomainDeformableRegistration()
  {
  }
  void PrintSelf(std::ostream& os, Indent indent) const;

  /** Exponential type */
  typedef ExponentialDisplacementFieldImageFilter<VelocityFieldType, DeformationFieldType> FieldExponentiatorType;

  typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;

  itkSetObjectMacro( Exponentiator, FieldExponentiatorType );
  itkGetObjectMacro( Exponentiator, FieldExponentiatorType );

  /** Generate output data by performing the registration
   * at each resolution level. */
  virtual void GenerateData();

  /** The current implementation of this class does not support
   * streaming. As such it requires the largest possible region
   * for the moving, fixed and input velocity field. */
  virtual void GenerateInputRequestedRegion();

  /** By default, the output velocity field has the same
   * spacing, origin and LargestPossibleRegion as the input/initial
   * velocity field. If the initial velocity field is not set, the output
   * information is copied from the fixed image. */
  virtual void GenerateOutputInformation();

  /** The current implementation of this class does not supprot
   * streaming. As such it produces the output for the largest
   * possible region. */
  virtual void EnlargeOutputRequestedRegion( DataObject *ptr );

  /** This method returns true to indicate that the registration should
   * terminate at the current resolution level. */
  virtual bool Halt();
  
  

private:
  MultiResolutionLogDomainDeformableRegistration(const Self &); // purposely not implemented
  void operator=(const Self &);                                 // purposely not implemented

  RegistrationPointer       m_RegistrationFilter;
  FixedImagePyramidPointer  m_FixedImagePyramid;
  MovingImagePyramidPointer m_MovingImagePyramid;
  FieldExpanderPointer      m_FieldExpander;
  VelocityFieldPointer      m_InitialVelocityField;

  unsigned int              m_NumberOfLevels;
  unsigned int              m_CurrentLevel;
  std::vector<unsigned int> m_NumberOfIterations;

  /** Flag to indicate user stop registration request. */
  bool m_StopRegistrationFlag;

  FieldExponentiatorPointer m_Exponentiator;
 
  /**
   * Regularization type.
   */
  unsigned int              m_RegularizationType;

  /**
   * Weight for the penalization of the harmonic energy.
   */
  float                     m_HarmonicWeight;

  /**
   * Weight for the penalization of the bending energy.
   */
  float                     m_BendingWeight;

 /**
 *    * Standard deviation for global field regularization
 *       */
  double                    m_StandardDeviations[ImageDimension];

  /**
 *    * Standard deviation for update field regularization
 *       */
  double                    m_UpdateFieldStandardDeviations[ImageDimension];

/**
 *    * Standard deviation for the similarity criteria
 *       */
  double                    m_SimilarityCriteriaStandardDeviations[ImageDimension];

/**
 *    * Trade-off coefficient
 *       */
  double                    m_SigmaI;


  /**
 *    * Unit of the standard deviation : true if it is world unit, false if it is voxel unit.
 *       */
  bool                      m_StandardDeviationWorldUnit;

  /**
 *    * Modes to control smoothing of the velocity field
 *       */
  bool                      m_SmoothVelocityField;

  /**
 *    * Modes to control smoothing of the velocity field
 *       */
  bool                      m_SmoothUpdateField;

};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMultiResolutionLogDomainDeformableRegistration.txx"
#endif

#endif
